Showing : GO • reset
1
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1
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91
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topGo error loading data
topGO GO
4 weeks ago peter • 0
2
votes
4
replies
278
views
question regarding installation of "enrichplot" with BiocManager
R BiocManager install clusterProfiler GO
written 8 weeks ago by • 0
0
votes
1
reply
133
views
Downstream analysis with Differentially Expressed Genes
DESeq2 GO goseq FunctionalAnnotation
updated 11 weeks ago by ▴ 10 • written 11 weeks ago by • 0
0
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1
reply
171
views
I want to convert the go enrichment result to a data frame (tidy data)with two column which one is the gene symbol and the other is go term. Any one…
GO.db GOfuncR GO GOSim goProfiles
updated 3 months ago by ▴ 530 • written 3 months ago by • 0
0
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0
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152
views
Gene Ontology on Streptococcus Pneumoniae genes sets
GO GeneOntology LocusIDtogeneIDconversion
3 months ago BioinFo.X • 0
0
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4
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329
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GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt GO ensembldb fgsea
3 months ago dario.beraldi • 0
2
votes
3
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426
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 4 months ago by ▴ 60 • written 4 months ago by ▴ 10
1
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3
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371
views
Trouble importing my own Gene Ontology Annotation into topGO
Annotation GeneOntology topGO GO
updated 7 months ago by 62k • written 7 months ago by ▴ 60
0
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13
replies
958
views
EnrichGO not working with db created from annotationhub
clusterProfiler AnnotationHubData GO
updated 8 months ago by ★ 3.5k • written 8 months ago by ▴ 10
0
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0
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232
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What exactly are Nontrivial node in topGO analysis?
topGO GO
9 months ago theophile • 0
0
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0
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1.1k
views
Create a Gene Enrichment GO plot from goana output
goana RNASeq edgeR RnaSeq GO
10 months ago Raito92 ▴ 60
15
votes
18
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1.2k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2 edgeR goana GO
updated 10 months ago by 47k • written 10 months ago by ▴ 60
0
votes
2
replies
382
views
Gene Onotology: Can't get the goana function to work
edgeR GO
10 months ago Adelyn • 0
0
votes
1
reply
571
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 12 months ago by 3.7k • written 12 months ago by • 0
0
votes
3
replies
819
views
using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 12 months ago by 47k • written 12 months ago by ▴ 70
1
vote
3
replies
844
views
GOstats - are significantly enriched GO terms with a small "size" meaningful?
GOstats GO RNASeq
updated 14 months ago by 62k • written 14 months ago by ▴ 10
2
votes
6
replies
668
views
Biomart's getBM returns no genes for an existing GO-term in grch38, and less then expected in grch37
GO biomaRt
updated 17 months ago by ★ 5.8k • written 17 months ago by • 0
0
votes
1
reply
376
views
Extracting Go-enrichment and pathway analysis from phytozome annotation file
RNASeq GO
updated 20 months ago by 62k • written 20 months ago by • 0
2
votes
2
replies
554
views
retrieve gene IDs from GO.db GO
GO GO.db
21 months ago • updated 20 months ago decppced • 0
0
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9
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994
views
The GO annotation of fugal species outside of 20 model organisms is outdated
GO biomartr annotation ensemble fungi
updated 20 months ago by 62k • written 21 months ago by • 0
2
votes
2
replies
1.3k
views
How to download KEGG pathways for list of enriched genes
RNASeqRData GO
23 months ago Wuschel ▴ 10
3
votes
8
replies
2.5k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler AnnotationHub GO uniprot
updated 10 months ago by ★ 3.5k • written 24 months ago by • 0
2
votes
0
replies
469
views
Saving the results of the topGO package as an R object (rda/rds file).
RNASeq GO topGO Pathways
24 months ago Ben ▴ 50
1
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1
reply
1.3k
views
topGO expected values showing NA
GO hgu133plus2 topGO GO hgu133plus2 topGO
updated 2.0 years ago by ▴ 10 • written 9.9 years ago by ▴ 340
2
votes
2
replies
587
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 2.1 years ago by 62k • written 2.1 years ago by • 0
2
votes
3
replies
522
views
Error in topGO analysis
software error topGO go
updated 2.4 years ago by 3.7k • written 2.4 years ago by • 0
3
votes
1
reply
2.8k
views
Warning message as converting gene Symbol to ENTREZID
go clusterprofiler
updated 2.6 years ago by 62k • written 2.6 years ago by ▴ 20
0
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0
replies
341
views
ViseaGO merge_enrich_terms ERROR
go
2.6 years ago zaza.inline • 0
0
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9
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825
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ReactomePA error graph
r rnaseq bulk GO ReactomePA
2.6 years ago camillab. ▴ 10
2
votes
2
replies
458
views
biomart webservice error when using data from Phytozome
software error go
2.6 years ago e.lopez-cortegano • 0
1
vote
5
replies
591
views
No enriched GO terms with 1000 more genes
clusterprofiler GO
2.6 years ago Ruixuan ▴ 10
0
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1
reply
467
views
incorrect number of dimensions in probeSetSummary function from GOstats
GOstats GO R
updated 2.6 years ago by 62k • written 2.6 years ago by ▴ 10
3
votes
6
replies
871
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 7 months ago by • 0 • written 2.7 years ago by ▴ 30
0
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5
replies
552
views
Error with using getBM function in biomaRt
go r software error R biomaRt
2.7 years ago morteza.aslanzadeh ▴ 30
1
vote
2
replies
426
views
About topGO error
go
updated 2.7 years ago by ▴ 30 • written 2.7 years ago by • 0
2
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4
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659
views
GO/KEEG enrichment for non-model bacteria - help for beginner
bacteria GO KEEG RNAseq
2.7 years ago liz.marjory • 0
0
votes
2
replies
305
views
GO analysis without gene IDs?
deseq2 annotation go
updated 2.8 years ago by 39k • written 2.8 years ago by ▴ 30
0
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0
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287
views
enrichplot pakage no output plot
go
2.8 years ago Hamidreza Hashemi ▴ 20
0
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1
reply
3.0k
views
GO of clusterprofiler
go
updated 2.8 years ago by 3.7k • written 2.8 years ago by • 0
1
vote
3
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836
views
TopGO significant genes
TopGO GO
2.8 years ago Al-a ▴ 10
5
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7
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959
views
Alternative tools to perform GO enrichment on DE genes
go de enrichment rnaseq goana
updated 2.8 years ago by 47k • written 2.8 years ago by ▴ 60
6
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6
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1.1k
views
GO enrichment analysis with goana after performing DE analysis with glmTreat
go DE edger rnaseq glmTreat
updated 2.8 years ago by 47k • written 2.8 years ago by ▴ 60
0
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1
reply
4.1k
views
Clusterprofiler error: No gene can be mapped
software error go annotation clusterProfiler
2.8 years ago tianshenbio • 0
0
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0
replies
427
views
How to identify differentially expressed genes from Reactome pathways enriched according to GOseq?
goseq go rna-seq
2.8 years ago hasse.bossenbroek • 0
0
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0
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283
views
ViSEAGO, merge_enrich_terms error
go
2.8 years ago m.n • 0
0
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4
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529
views
<N/A> Gene Ontology while using the AnnotationDbi package
go annotation annotationdbi
2.8 years ago CUCIO199 • 0
2
votes
4
replies
1.0k
views
How to get list of all GOIDs with all genes in each GO term?
go annotation
updated 2.9 years ago by 62k • written 2.9 years ago by • 0
1
vote
3
replies
437
views
Extract the relevant information of the genes sets from the Bioconductor annotation package
org.Rn.eg.db annotation go
updated 2.9 years ago by 62k • written 2.9 years ago by • 0
0
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0
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262
views
Program to calculate genetic distances with long sequences
probe go
2.9 years ago antoniorevail • 0
0
votes
0
replies
405
views
News: RNAseq data analysis with R and Bioconductor
limma deseq2 go edger News
2.9 years ago info ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: transcript name mapping between human and mouse by Eric • 0
It works very well, and thanks for such a great answer! Because I use the old version gtf from GENECODE (vM12), the id version does not mat…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads by Bernardo • 0
Just did that, thank you for the suggestion.
Comment: Empty ChipQC Report by Okan • 0
Hi, I have the same issue. Have you found any solution or any reason why this is happening?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Votes
Answer: transcript name mapping between human and mouse
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
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